Amaya
by StupidMajor
Summary: While on a dilithium mining mission, Kathryn runs into a surprise. ChakotayKathryn. [COMPLETED]
1. Prologue

**Title: **Amaya

**Summary: **While on a dilithium mining mission, Kathryn runs into a surprise. ChakotayKathryn

**Disclaimer: **I do not own Voyager or its crew sadly :'( ... i only own what was not in the series (you'll find out soon)

* * *

**Prologue**

The Federation Starship Voyager drifted through the nebula slowly. What normally was just a beautiful interstellar phenomenon, was now their only chance for survival. A week had passed since Captain Janeway and crew had to take refugee in the sensor blinding cloud. A week full of repairs and stress.

Repairs were going extremely slow. They barely had energy to raise shields, let alone to fire a phaser. The unknown alien attack had left them extremely vulnerable and beaten up. They were literally dead in the water, the only thing moving them were the currents of gas and phosphor in the nebula. Their chances for a dilithium refit had been taken away. Voyager couldn't function without it. It was essential. Before entering the could, they had discovered a source of dilithium on a planet near the cloud. The only problem was, the ship wont be going anywhere until Engineering got impulse and the warp coil to work.

B'Elanna Torres took a short breath and impatiently blew at a strand of hair that had fallen across her eyes. She was on her knees and elbow deep inside a relay station and the recalcitrant wisp was just one more irritation in a series of annoyances that had plagued her all morning. She made one last adjustment to  
the EPS network, stood up, and turned to her control station.

"Okay, let's do it again."

"Yes ma'am." Harry Kim replied and she rewarded him with a glare that would have done Kathryn Janeway proud.

"That's not funny Harry. We're sitting ducks right now. The warp core's off line and we can barely move at impulse. I promised the captain I'd get the defense system recalibrated and back up and running today, and I'm going to do it."

Voyager's engineering staff moved quickly and efficiently to obey her orders. She had promised them all extra time off if they met her deadline, and besides Lieutenant Torres was on a tear today, and no one wanted to incur her displeasure.

"Harry, we can get this to work. Adjust for gravimetric shear another three degrees. That should reduce the pulse and eliminate the reverberation."

Harry's fingers flew over his console as he made the corrections she requested.

"Activate the conversion matrix and begin the countdown. Let's go."

"Activated."

"Countdown to begin on my mark." She paused for a moment and made another entry on her console. "Now."

"Counting down from 10 seconds" Harry responded.

Voyager vibrated again as she sent another shockwave out into space.

"Damn." B'Elanna checked the readings on her console. "Harry, are you sure you made it exactly three degrees? Check the.."

"B'Elanna, I've adjusted it six times, exactly to your specifications. Maybe we should take a break."

"I don't need a break. I need this to work. Seven"

"I am here Lieutenant." The former drone appeared almost immediately at B'Elanna's elbow.

"I asked you to realign the deflector to compensate for the neutrino bursts."

"I have done as you directed Lieutenant. The problem is not with the deflector."

"Don't tell me what the problem isn't. Let's find out what the problem is."

She tossed her a PADD that had been resting on the edge of her console.

"Here. See if your Borg ingenuity can come up with a solution."

Seven of Nine raised an eyebrow and looked at Harry Kim, who just grinned and shrugged. Seven held his gaze for a second and then looked down at the PADD.

"In the meantime Harry," Torres turned and addressed him again. "Divert the neutrino emissions into the exhaust system."

"I'm due back on the bridge in five minutes B'El"

She glared at him again.

Harry nodded and did as he was ordered.

"Fire."

The ship shuddered even more violently than the last time as another wave of energy was thrown out into the void.

All three of them watched the readings as they appeared on the screen in front of them.

"Janeway to Torres. What's going on down there, Lieutenant?" Kathryn Janeway's voice came over the comm system.

"Captain, it's taking a little longer than I thought to work the kinks out of the matter conversion matrix. I'm trying to rebuild the entire defense system here."

"I appreciate what you're doing B'Elanna. I just want to make sure Voyager survives the improvements."

"Captain, your ship will be just fine." Torres out. She slapped at her comm badge and turned back to her console.

Harry sighed. It was going to be a long shift.


	2. I Thought You Said

**I Thought You Said There Were No Human Life Forms On This Planet!**

"Coffee, black."

A cup of steaming hot coffee instantly materialized, and Kathryn picked it up, savoring the aroma. Outside the ready room window, stars flew by at warp speed, and Kathryn gazed at them a moment before making her way to her desk. Just as she was about to sit down, the doors opened and Chakotay came in. Kathryn smiled warmly. "Good morning."

Chakotay smiled in return. "Good morning. I bring good news."

"You've found a way to get us home?" Kathryn said half-teasing, half-serious.

"No, not as good. B'Elanna just got the warp core and impulse engines online."

Kathryn stood up and smiled, "Great, go tell Tom to set course towards the planet. We might to be doing some mining."

* * *

"Energize," Kathryn said. In a matter of seconds, she and the first group of away team were on the planet. They had gotten lucky. The planet was M Class and looked much like Earth. Tropical rainforests, hot deserts, beaches, everything but it was not the real Earth. No human life forms though, just a couple of wild birds.

"We could take a vacation here!" Tom exclaimed.

Kathryn laughed, "If you keep that up, you might just convince me." Kathryn scanned the area and pointed in a direction south "The readings are coming from that directions, towards the mountain." She said and headed of, Chakotay right beside her and Tom, Tuvok, and B'Elanna following.

"It would be nice to take a vacation here, don't you think?" Kathryn asked.

"Yes. It would give the crew a chance to relax for a while, giving the circumstances on this past month. They deserve it."

"Right. Tom, when we get back, tell the crew to thank you." She said over her shoulder.

"Why Captain?"

"Vacation Tom! Ever heard of it?" Kathryn joked.

Tom laughed. "Yes ma'am!"

The rest of the journey was quiet except for an occasional small talk. When they reached the mountains, Tuvok scanned the perimeter. "Captain, there is an entrance approximately one mile right. The is the only entrance and the dilithium is inside."

"Alright, lets go." Kathryn said, but a noise to her left stopped her. She drew her laser, as did everyone else.

"Hello?" Chakotay said into the thick dense forest surrounding the mountains.

Silence.

Then there was more rustling and they heard a branch break.

Then nothing.

"Anyone?"

"My tricorder's not picking up any life signs except birds," Chakotay replied, scanning the area thoroughly.

Kathryn sighed and turned back to the away team. She was about to speak when Chakotay spoke up. Wait a minute," he said. "I'm picking up something."

Kathryn moved over to his position and, as she did so, found her tricorder picked up a life sign aswell.

"500 yards away," she said. "Immature female….human."

Chakotay looked up at her. "How is that possible? I thought you said there were no human life forms on the planet?"

"I don't know," Kathryn replied. "Perhaps our sensors were unable to detect them for some reason."

"I agree Captain," Tom said and B'Elanna nodded.

"Right. Looks like we're not going to have that vacation after all, but we need the dilithium. Any suggestions?"

"I believe we should go back to the ship Captain. We are already in vile of the Prime Directive."

"What if she's the only one here. We cant just leave her here!" B'Elanna argued.

Kathryn sighed, "Tuvok, you, Tom, and B'Elanna go back to the ship. Chakotay and I will look for the girl."

"Captain.."

"No buts Tuvok. B'Elanna might be right. She could be the only one here. Go." As soon as they were gone from sight, she turned to her fist officer. "Lead the way."


	3. Amaya

**Amaya**

After - what seemed like hours - of wading quickly through dense woodland, they saw an opening in the trees ahead. On the ground a few yards away, curled up, was what appeared to be a little girl, the human equivalent of a five or six year old. Long blond hair fell over what was otherwise a naked body. A growl emitted from their left. There, upon a rock, was a large black panther. The animal was glaring at the child with an unmistakably predatory look in her eyes. With a steady hand, Chakotay aimed his phaser at the animal and fired. Instantly, the panther fell to the ground unconscious.

Kathryn then hurried over to the little girl. Tears stained her cheeks and her snow white body was painfully thin and covered in bruises.

"Janeway to transporter room one, three to beam directly to sick bay," with that they were gone.

* * *

"Multiple fractures and bruises and malnutrition."

"Is she going to be alright?" Kathryn asked.

"Yes, but there's one more thing. She's deaf. When I tried to create a suitable hearing aid, she woke up and ran."

Kathryn eyes grew wide with worry, "Where is she now?"

"Follow me," The Doctor walked to the farthest edge of sickbay, and there, right under a small desk, was the little girl. Her arms were wrapped around her knees and her face in the cave her legs made. "Every time I go near her, she runs."

Kathryn sighed, "Let me try."

"Go right ahead," he said and backed away. Kathryn slowly approached the girl and squatted down to her size. They young girl, sensing a presence, raised her head and back further into the wall.

'_I hope this works," _Kathryn thought and held up her hands.

"_Hello. Do not be afraid, we will not harm you. I am Kathryn Janeway. What is your name?" _Kathryn easily signed to the girl.

The girl made no sign of understanding, but after a few minutes, the girl replied, _"Amaya."_

"_Night rain, such a beautiful name."_

"_Kathryn. Pure. I like it."_

"_Thank you. Is it alright if I ask you questions?" _

Amaya nodded.

"_Our Doctor, the bald guy over there, was healing you and wanted to heal your deafness, but you ran away every time he tried, why is that?"_

"_I want to be deaf, it is who I am. I was born this way and I have accepted it. It created my personality."_

"_Your very smart sweetheart."_

Amaya smiled, _"Thank you."_

Kathryn turned to the EMH. "Is she mute Doctor?"

"No Captain, she is fully able to speak. I think it is the traumatic experience so cause her not to speak."

Kathryn nodded and turned back to Amaya, _"Amaya, what happened to your people?"_

"_They kept us in a prison, treated us badly, and then took people week by week to the planet. We were the last ones. No more after us. They took us to the planet, beat us, and then abandoned us." _Tears welled in her eyes. _"Mama died trying to save our people." _Tears not fell freely from her eyes and she sobbed. Kathryn scooped her up in her arms and comforted the little girl. She rocked the girl back and forth and hummed a song she knew by heart, even as she knew the girl could not hear. The crying soon turned into hiccups which turned into silence. Kathryn looked down at Amaya and found she was asleep.

Carefully, with ought waking her, Kathryn got up from the floor and went over to the Doctor.

"Is it alright.." The EMH put up his hand to stop the Captain in mid speech.

"Its alright. She is better suited in an environment with people she trusts Captain." Kathryn nodded her thanks and headed out of sickbay, carrying the sleeping Amaya all the way.

* * *

**i know its short and im sorry. every since ive been back in school things have been further and further behind. but dont worry. review and everything will be just fine!!  
**

**hugs and kisses**

**Sammy**


	4. All I Ever Wanted

**All I Ever Wanted**

A week had passed since they found little Amaya stranded on the planet. She was still shy, hanging around Kathryn, and surprisingly Chakotay.

'_It has only been a week,' _Kathryn mused as she leaned back against her chair. Amaya was curled in a tight ball, asleep, on the couch in her ready room. She had fallen asleep while Kathryn was on duty, and Kathryn didn't have the heart to wake her.

The plan was that Amaya had the bed and Kathryn took the couch, until the room was redone. But the first night, Amaya had a terrible nightmare and Kathryn ended up sleeping with her. Every since then, she never left the little girls side while she was sleeping.

The ready room door chimed. "Enter." She looked up to see Commander Chakotay enter. He smiled and he saw Kathryn and Amaya. "Report."

"It's a quite night. Nothing to report."

"Good. Anything else?"

"I'm having dinner at my place tonight at 1900, would you like to join me. Amaya is invited too."

"I might just take up that offer."

"Great. See you tonight." With that he left. As soon as the doors closed, Kathryn let out a breath she didn't know she was holding. '_If only he knew.'

* * *

_

A beautiful crimson nebula glowed in the distance. Amaya had fallen asleep again on the couch right after dinner. Kathryn watched Chakotay gaze at it as they sat together at a dining table in his quarters. Amaya had fallen asleep again on the couch right after dinner. The red tone of the nebula reflected on his face and the white shirt he was wearing. His eyes were fixed on the natural wonder but his thoughts seemed a million light years away. He had been quiet all evening and they had eaten in virtual silence.

"Chakotay," she said quietly. It was now or never.

He turned away from the window to face her.

"The other day," she continued, "I was thinking. What if no one cares about us, what if they all give up."

Chakotay looked up at her now and took her hand in his. "I care, Kathryn," he said quietly. "You've dedicated your life to Starfleet and are the most incredible captain I've ever known. When we get home, you deserve to be welcomed as a heroine and decorated with all the honors possible. You don't deserve to be looked upon with disapproval and contempt."

"I haven't done any of this to be a heroine," Kathryn replied, "or to be showered with honors. Everything I've done is for this crew. They are all that matter to me."

"And you are the only one that matters to me."

"Chak-"

"No. I'm tired of lying to myself and hiding from you. But we can't, Starfleet wouldn't approve."

"I don't give a damn about Starfleet!" Kathryn's voice rose.

"Even if it cost you your rank?"

"Even then."

He shook his head sadly and turned away from her. He got to his feet and wondered over to the window. "No you wouldn't," he said quietly. "You would end up resenting me and I would resent myself. I love you too much to ask such a sacrifice of you."

Kathryn got up slowly and walked over to him.

"It wouldn't be a sacrifice," she answered. "It would be a privilege." She paused. "You've only ever treated me with kindness, respect ... and love."

Chakotay turned to her and his unshed tears sparkled crimson in the glow of the nebula.

She turned to him slowly and saw her own pain mirrored in his eyes. "We know the risks," she said quietly. "We know if we're captured by an enemy they won't be kind to us." Tears welled in her eyes. "All part and parcel of the job."

Her lips trembled and Chakotay saw her unspoken pain in her eyes. He gently gathered her in his arms and Kathryn accepted the embrace he offered, holding him in return.

It was a while before they drew away, neither wanting to let go, both just wanting to stay locked in the other's arms.

"I haven't been intimate with a man since," Kathryn said at last. "You can't go through something like that and not be affected, and I changed afterwards, withdrew myself. I needed to be alone, come to terms with it. Mark didn't understand. He tried, but he didn't. We separated for a while, over a year, and then just before I got promoted to Captain, we decided to give things another go. He asked me to marry him, I think as a way of showing how committed he was to me, but our relationship was still difficult, and neither of us rushed to set a date. There was a barrier between us that had never existed before and we didn't seem able to take our relationship beyond a certain point."

All the things that had puzzled Chakotay over the years were finally beginning to make sense now. This was clearly another reason she had held back from him. He felt humbled and ashamed, ashamed that he'd misread the signs and made wrong assumptions.

"I'm sorry," he whispered. "I'm so sorry that I made wrong assumptions."

"We both have, Chakotay. I thought you didn't say anything because you didn't care any more. But the whole time you were silent because you did." She paused. "I'm scared, Chakotay. I'm scared of so many things. I'm scared of loving you only to lose you. I'm scared of not being enough for you and scared at the same time of being too much. I'm even scared sometimes at just how deeply I love and need you. Because I do, Chakotay. I need you." Her voice fell to a whisper. "Please don't reject Kathryn because of the captain..."

Chakotay tenderly put his hand to her cheek. "Kathryn's all I want," he said sincerely. "All I've ever wanted."

Kathryn smiled softly and took his hand in hers. "Whatever happens when we get home, we'll face together. It doesn't matter what anyone will think. It really doesn't. All that matters is how the crew would feel about us being together and every instinct tells me they wouldn't object."

"Of course not," Chakotay answered. "They know how dedicated we both are to getting them home."

"Then shall we call a meeting tomorrow and tell them we would like to pursue a relationship if we have their consent?"

Chakotay nodded with a smile. "First thing in the morning."

He then drew Kathryn close again and she leant her head on his broad shoulder. She closed her eyes as his arms enfolded her and Chakotay held her tight, wishing he could hold her safe in his arms forever.

* * *

**chapter 3 is done..yay!! tell me what you think. am i rushing...i dunno..it might be just me.**

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p.s. as of yet, there are no fanfiction, but there soon will be! still, check it out


	5. A New Daddy

**A New Daddy**

The senior staff laughed and talked as they piled into the briefing room for what they thought was a routine meeting. Kathryn stood between the window and the table with Amaya and watched as they all entered and took their seats. Chakotay, who was already seated, could tell she was more worried about what their reaction would be than she was letting on. She was pale, and her fingers kept fidgeting with her commbadge.

Harry approached Kathryn. "Seven and the Doctor can't make it, Captain. Something's come up in sickbay. Something with Icheb, I think."

Kathryn gave a nod. "Thank you for telling me."

At last, everyone was seated and all eyes lay on the captain. Kathryn nervously cleared her throat, and then began to speak.

"Commander Chakotay and I have summoned you here this morning because we would like to discuss something with you." She paused. "As you know, because of our situation, I have lifted the protocol issue regarding personal relationships. Relationships are permitted so long as they are conducted maturely and providing that the Commander and I are informed of any attachments. This is absolutely vital to maintaining professionalism, and so far many crew members have been able to successfully combine both a professional and a personal relationship." She paused uncomfortably. "Commander Chakotay and I ... we ... we have come to realize that we care for each other very much and we would like to pursue a personal relationship."

At this, the senior staff turned to look at each other, but said nothing.

Before Katherine or Chakotay could say anything else everyone leaped up from their seats and rushed over to congratulate them. Katherine smiled and realized that she was able to relax. She hadn't heard so many congratulations in her life.

She waited for at least one question, perhaps even a concern.

But there were none.

The only sound that greeted her ears was amused laughter.

Kathryn stared at her officers in confusion. Her eyes met Harry's and he smiled warmly. "Forgive us, Captain, but we've all long guessed how you and the Commander feel about each other. We've just wondered how long it would take you both to realize it."

Kathryn felt her cheeks blaze from a feeling of foolishness, but she also felt a sense of relief.

Tom got up from his chair and went over to her. "You'll find no opposition from anyone on this ship, Captain. Everyone thinks highly of you and the Commander and would like you to be happy."

A tug on her pant leg brought her attention to the 'little captain', as everyone was calling her.

"_Amaya have mommy and now daddy?"_

Kathryn laughed, _"Yes my little captain." _

Amaya smiled and hugged her 'mother' and ran over to her new 'father', who picked her up and spun her around. "How about after duty, how 'bout we take a little family bonding?"

Before Kathryn could answer, the ship trembled. "Red alert. All hands to battle stations."

Chakotay an Kathryn exchanged look and ran to get to the bridge. "Report!"

"Unknown species attacked unprovoked." Tuvok answered. "They are equal to us in technology."

"Hail them." After a few moments, Tuvok's console beeped. "Answering to our hail."

"On screen."

The black screen took the appearance of a green alien. He had a Klingon face, but Vulcan or maybe Romulan ears. "I am Captain Ta'Ku of the Planet Kunan. You have our prisoner. Give her back immediately or we will be forced to take her by force."

"I am Captain Janeway. I am sorry Captain, but we have no prisoner of yours."

"Like hell you don't!" Ta'Ku grunted. "What do you call that." He said and pointed to a figure behind her. A little head poked itself from behind Kathryn. The head belonged to Amaya.

"We saved this girl from death. She is not yours."

"She is mine! I bought her, she was my slave, and is now a prisoner! She will die for what she has done to our people."

"I will not give her up, I do not believe you. This girl could not have done anything to your people."

"I am sorry Captain, but if you will not give her up, I will take her by force." He said and was about to end the transmition when a small voice spoke up.

"No!" Amaya stepped out from behind Kathryn. "I will not let you harm my family!"

Ta'Ku laughed, "What are you going to do prisoner, shoot at us. Hah! You make me laugh!"

Kathryn walked up to her daughter and held her with an arm, "She might not do anything, but her mother sure will. Tuvok, fire three photon torpedoes at their port side."

Tuvok nodded and fired. "Their shields are failing."

Kathryn smirked at the alien, "Another hit and you will be done."

Ta'Ku stuttered, "You-you would."

"Tuvok…"

"I-I- I am sorry for stopping you Captain. I hope you have a safe trip." He said and the screen turned black.

"Commander you have the bridge. I am taking Amaya home." Without a reply, Kathryn left with her daughter.


	6. Riddle

**Riddle**

"Mommy! Mommy!" A now six year old Amaya squealed as her mom entered the their quarters. It was three months after the run in with Ta'Ku and Amaya's first time talking.

"_Hey there my little Captain. Where's daddy?"_

"Daddy is with Uncle Tom and Aunt Nanna. Daddy said Uncle Tom was bad and wrecked the Delta Flyer."

Kathryn laughed. _"That's what I heard too. Now, you hungry?" _Amaya nodded. _"What do you want?"_

"Mac and Cheese!" Her favorite food. 'Uncle' Tom had introduced it to her while he and B'Elanna were babysitting her. She has been hooked every since.

"_Alright, Mac and Cheese it is." _Kathryn went over to the replicator and replicated the meal and set it on the dining table. Amaya sat down and began to eat.

Kathryn was watching her daughter each when a pair of strong arms went around her waist.

"Guess who."

Kathryn turned around in her lover's arms and kissed him. "Missed you."

"Missed you more." Chakotay kissed her passionately, until it was interrupted by a 'ewww'. They broke apart and looked at their daughter and smiled.

"Eat, or no cake," Kathryn said and Amaya dug back into her food. Kathryn looked back to Chakotay. "Not that I got that settled, I have a riddle for you: What do you get when you cross a Maquis rebel with a Starfleet Captain?"

"A freedom fighter who looks good in uniform?" Chakotay suggested dryly.

"No, but I'll give you a hint. There's only two possible answers."

"And those would be?"

Janeway smiled. "A boy or a girl."

It took a moment for Janeway's answer to register, and when it did, Chakotay shot her a surprised look. "You're pregnant?" he prompted incredulously.

Janeway nodded in silent confirmation, earning her a delighted yell from Chakotay. Getting to his feet, Chakotay walked around the table and pulled her into his arms, then gave her a deep, lingering kiss. After several minutes, Chakotay broke off the kiss and lifted his hands to cup her face. "We're having a baby," he whispered in wonderment.

The reverence in his tone brought tears to Janeway's eyes, and in a deliberate imitation of his favorite gesture, she gently placed her hand against his cheek.

"I love you," she said softly.

"I love you."

"I get a baby brother or sister?" Amaya asked. Kathryn bent down to her daughters level and nodded. Amaya squealed and launched herself in her mothers arms. "I take it we got her approval." She stood up with their daughter in her arms.

"We're a family."

Chakotay smiled. "And I wouldn't have it any other way."


End file.
